Thanks for the response.
Let me rephrase my question.
Will mailboxes created via ISPConfig work only with a webmail client? Can I not use POP3 or IMAP to access those mailboxes?
I installed one of the recommended webmail clients (UebiMiau) and i am able to send and receive email fine. But I want to configure it in such a way that I can send and receive email using Thunderbird etc.
Yes, I have enabled Maildir option under "Management -> Server -> Settings -> EMail"